PmagPy Command Line Version¶
This notebook demonstrates the use of PmagPy command line scripts. Additional background and documentation can be found in the PmagPy Cookbook.
What is PmagPy?¶
PmagPy is a software package for analyzing paleomagnetic and rock magnetic data using Python. If you need to install Python and PmagPy locally, follow the install instructions. This notebook demonstrates the use of PmagPy functions on the command line. For examples of how to use PmagPy scripts in a Python environment, see the static version of PmagPy.ipynb or if you are running jupyter notebook, you can open it locally.
What are paleomagnetism and rock magnetism?¶
For information on the science of paleomagnetism and rock magnetism, see Essentials of Paleomagnetism.
Running this notebook¶
You are currently looking at static html, but you may want to run this notebook interactively. To do so, you'll need to first install Python and PmagPy (see the Cookbook for install instructions). You can then launch the notebook from your command line with the following commands.
cd Desktop
move_data_files.py
cd PmagPy-data
jupyter notebook
jupyter notebook will open a browser window, and you can then click on the notebook you want to run (like this one or the PmagPy_cli notebook).
Note: You only have to do the move_data_files.py command once after initial installion and then once after each update. You should make a copy of any notebook (see File menu) if you want to make any changes as each update will overwrite the standard notebooks.
Getting started¶
In [1]:
import os
import glob
from IPython.display import Image
import matplotlib as plt
from pmagpy import pmag
basemap_present, Basemap = pmag.import_basemap()
cartopy_present, cartopy = pmag.import_cartopy()
from pmag_env import set_env
Help¶
You can get more details about any program on your command line or in a notebook. There are many options available for each program, all of which are listed in each program's help message. To call up the help message, you just need to use the command line argument -h. See the examples below:
To get help within the notebook environment:
! program_name.py -h
To get help on the command line:
program_name.py -h
If you are running Windows, you may need to run:
program_name -h
Here's an example of calling up the help message for program angle.py:
In [2]:
!angle.py -h
Guide to PmagPy¶
- the functions in this notebook are listed alphabetically so here is a handy guide by function:
Calculations:
- angle.py : calculates the angle between two vectors
- apwp.py : returns predicted paleolatitudes, directions and pole latitude/longitude from apparent polar wander paths of Besse and Courtillot (2002).
- b_vdm.py : converts B (in microT) and (magnetic) latitude to V(A)DM (see vdm_b.py)
- bootams.py : calculates bootstrap statistics for tensor data
- cart_dir.py : converts cartesian coordinates (x,y,z) to declination, inclination, intensity (see dir_cart.py)
- di_eq.py : maps declination, inclinatitions to X,Y for plotting in equal area projections
- di_geo.py : rotates declination, inclination in specimen coordinates to geographic
- di_rot.py : rotates directions to a coordinate system with D,I as center
- di_tilt.py : rotates directions to stratigraphic coordinates
- di_vgp.py : converts direction to Virtual Geomagnetic Pole (see vgp_di.py)
- dia_vgp.py : converts direction and $\alpha_{95}$ to Virtual Geomagnetic Pole and dp,dm
- dipole_pinc.py : calculates inclination given latitude assuming geocentric axial dipole
- dipole_plat.py : calculates latitude given inclination assuming geocentric axial dipole
- dir_cart.py : converts declination, inclination, intensity to cartesian coordinates (see cart_dir.py)
- eigs_s.py : converts eigenparameters to equivalent 6 element tensor (see s_eigs.py)
- eq_di.py : takes X,Y from equal area projection (e.g., from digitized coordinates) and converts to declination, inclination
- fcalc.py : returns the value from an F table, given the degrees of freedom.
- fisher.py : generates sets of directions drawn from Fisher distributions with vertical true mean
- fishrot.py : generates sets of directions drawn from Fisher distributions with arbitrary true mean
- gaussian.py : generates data drawn from a normal distribution
- gobing.py : calculates Bingham statistics from a set of directions
- gofish.py : calculates Fisher statistics from a set of directions
- gokent.py : calculates Kent statistics from a set of directions
- goprinc.py : calculates principal directions statistics
- igrf.py : calculates geomagnetic field vectors for location, age given a field model (e.g., IGRF)
- incfish.py : estimates the true mean inclination from inclination only data
- pca.py : calculates the best-fit line or plane for demagnetization data and associated statistics
- pt_rot.py : rotates point given finite rotation pole
- scalc.py : calculates VGP scatter
- s_eigs.py : takes a 6 element tensor and calculates eigen parameters (see eigs_s.py)
- s_geo.py : rotates 6 element tensors to geographic coordinates
- s_hext.py : calculates Hext statistics from 6 element tensors
- s_tilt.py : rotates 6 element tensors to stratigraphic coordinates
- squish.py: flattens inclination data given flattening factor (see unsquish.py)
- sundec.py : calulates direction to sun for location, date, time and sun azimuth
- tk03.py : generates sets of directions consistent with the TK03 field model
- uniform.py : generates sets of uniformly distributed directions
- unsquish.py : unsquishes flattened inclinations, given flattening factor (see squish.py)
- vector_mean : calculates vector mean for sets of vectors (declination, inclination, intensity)
- vdm_b.py : calculates intensity at given location from specified virtual dipole moment (see b_vdm.py)
- vgp_di.py : calculates direction at given location from virtual geomagnetic pole (see di_vgp.py)
- watsons_f.py : calculates Watson's F statistic for testing for common mean
Plots:
- ani_depthplot.py : plots anisotropy data against depth in stratigraphic section (Xmas tree plots)
- aniso_magic.py : makes plots of anisotropy data and bootstrapped confidences
- biplot_magic.py : plots different columns against each other in MagIC formatted data files
- chi_magic.py : plots magnetic susceptibility data in MagIC format as function of field, frequency or temperature
- common_mean.py : graphical approach to testing two sets of directions for common mean using bootstrap
- core_depthplot.py : plots MagIC formatted data
- curie.py : makes plots of Curie Temperature data and provides estimates for Tc
- dayplot_magic.py : makes Day et al. (1977) and other plots with hysteresis statistics
- dmag_magic.py : plots remanence against demagnetization step for MagIC formatted files
- eqarea.py and eqarea_magic.py : makes equal area projections for directions
- eqarea_ell.py : makes equal area projections for directions with specified confidence ellipses
- find_ei.py : finds the inclination unflattening factor that unsquishes directions to match TK03 distribution
- fishqq.py: makes a Quantile-Quantile plot for directions against uniform and exponential distributions
- foldtest.py & foldtest_magic.py : finds tilt correction that maximizes concentration of directions, with bootstrap confidence bounds.
- forc_diagram.py: plots FORC diagrams for both conventional and irregular FORCs
- hysteresis_magic.py : makes plots of hysteresis data (not FORCs).
- irm_unmix.py : analyzes IRM acquisition data in terms of coercivity distributions
- irmaq_magic.py : plots IRM acquistion data
- lnp_magic.py : plots lines and planes for site level data and calculates best fit mean and alpha_95
- lowes.py : makes a plot of the Lowe's spectrum for a geomagnetic field model
- lowrie.py and lowrie_magic.py : makes plots of Lowrie's (1990) 3D-IRM demagnetization experiments
- plot_cdf.py : makes a cumulative distribution plot of data
- plotdi_a.py : makes equal are plots of directions and their $\alpha_{95}$s
- plot_geomagia.py : makes plots from files downloaded from the geomagia website
- plot_magic_keys.py : plots data from MagIC formatted data files
- qqplot.py : makes a Quantile-Quantile plot for data against a normal distribution
- qqunf.py : makes a Quantile-Quantile plot for data against a uniform distribution
- revtest.py & revtest_magic.py : performs a bootstrap reversals test
- thellier_magic.py : makes plots of thellier-thellier data.
- watsons_v.py : makes a graph for Watson's V test for common mean
- zeq.py and zeq_magic.py : makes quicky zijderveld plots for measurement data
Maps:
- cont_rot.py : makes plots of continents after rotation to specified coordinate system
- plot_mag_map.py : makes a color contour plot of geomagnetic field models
- plot_map_pts.py : plots points on maps
- polemap_magic.py : reads in MagIC formatted file with paleomagnetic poles and plots them
- vgpmap_magic.py : reads in MagIC formatted file with virtual geomagnetic poles and plots them
Working with MagIC:
- combine_magic.py : combines two MagIC formatted files of same type
- grab_magic_key.py : prints out a single column from a MagIC format file
- magic_select.py : selects data from MagIC format file given conditions (e.g., method_codes contain string)
- download_magic.py : unpacks a contribution text file downloaded from the MagIC website
- upload_magic.py : prepares a directory with a MagIC contribution for uploading to MagIC
- Conversion scripts : convert many laboratory measurement formats to the MagIC data model 3 format
- _2g_bin_magic.py : converts 2G binary files to MagIC
- aarm_magic.py : takes a MagIC formated measurements.txt file with anisotropy of ARM data and calculates the tensors and stores in a MagIC formatted specimens.txt file.
- atrm_magic.py : takes a MagIC formated measurements.txt file with anisotropy of TRM data and calculates the tensors and stores in a MagIC formatted specimens.txt file.
- agm_magic.py : converts Princeton Measurements alternating gradient force magnetization (AGM) files to MagIC.
- bgc_magic.py : convert Berkeley Geochronology Center files to MagIC.
- cit_magic.py : convert Cal Tech format files to MagIC.
- generic_magic.py : converts generic files to MagIC.
- huji_magic.py : converts Hebrew University, Jerusalem, Israel files to MagIC.
- huji_sample_magic.py : converts HUJI files to a MagIC format.
- jr6_jr6_magic.py : converts the AGICO JR6 spinner .jr6 files to MagIC
- jr6_txt_magic.py : converts the AGICO JR6 .txt files to MagIC
- k15_magic.py : converts 15 measurement anisotropy of magnetic susceptibility files to MagIC.
- ldeo_magic.py : converts Lamont-Doherty files to MagIC.
- livdb_magic.py : converts Liverpool files to MagIC.
- mst_magic.py : converts Curie Temperature experimental data to MagIC
- sio_magic.py : converts Scripps Institution of Oceanography data files to MagIC
- sufar4_magic.py : converts AGICO SUFAR program (ver.1.2.) ascii files to MagIC
- tdt_magic.py : converts Thellier Tool files to MagIC
- utrecht_magic.py : converts Fort Hoofddijk, Utrecht University Robot files to MagIC
- orientation_magic.py : converts an "orient.txt" formatted file with field notebook information into MagIC formatted files
- azdip_magic.py : converts an "azdip" formatted file to a samples.txt file format
- other handy scripts
- chartmaker.py : script for making chart to guide IZZI lab experiment
_2g_bin_magic.py¶
In [3]:
!_2g_bin_magic.py -f data_files/convert_2_magic/2G_bin_magic/mn1/mn001-1a.dat
aarm_magic.py¶
In [4]:
# with data model 3
if os.path.exists('data_files/aarm_magic/specimens.txt'):
os.remove('data_files/aarm_magic/specimens.txt')
!sio_magic.py -f data_files/aarm_magic/arm_magic_example.dat -loc Bushveld -LP AF:ANI \
-ncn 3 ac 180 -dc 50 -1 -1 -F data_files/aarm_magic/measurements.txt
!aarm_magic.py -DM 3 -WD data_files/aarm_magic/ -f measurements.txt
!cat data_files/aarm_magic/specimens.txt | head
In [5]:
# with data model 2
!sio_magic2.py -f data_files/aarm_magic/arm_magic_example.dat -loc Bushveld -LP AF:ANI \
-F data_files/aarm_magic/aarm_measurements.txt -ncn 3 -ac 180 -dc 50 -1 -1
!aarm_magic.py -DM 2 -f data_files/aarm_magic/aarm_measurements.txt
agm_magic.py¶
In [6]:
# note: example data files are in old format
!agm_magic.py -spn myspec --usr ‘‘Lima Tango‘‘ -f data_files/convert_2_magic/agm_magic/agm_magic_example.agm -u cgs -old
angle.py¶
In [7]:
!angle.py -f data_files/angle/angle.dat
ani_depthplot.py¶
In [8]:
# OSX users with pip install should use:
#!ani_depthplot_anaconda -f data_files/ani_depthplot/rmag_anisotropy.txt -fsa data_files/ani_depthplot/er_samples.txt \
# -fb data_files/ani_depthplot/magic_measurements.txt -sav -fmt png -DM 2
!ani_depthplot.py -f data_files/ani_depthplot/rmag_anisotropy.txt -fsa data_files/ani_depthplot/er_samples.txt \
-fb data_files/ani_depthplot/magic_measurements.txt -sav -fmt png -DM 2
#Image(filename='U1361A_ani_depthplot.png')
In [9]:
# OSX users with pip install should use:
# !ani_depthplot_anaconda -DM 3 -WD data_files/ani_depthplot -sav -fmt png
os.remove('U1361A_ani_depthplot.png')
!ani_depthplot.py -DM 3 -WD data_files/ani_depthplot -sav -fmt png
Image('U1361A_ani_depthplot.png')
Out[9]:
aniso_magic.py¶
In [10]:
!aniso_magic.py -WD data_files/aniso_magic -crd s -f sed_specimens.txt -sav -fmt png -v -d 3 0 90 -n 300
In [11]:
Image("_g_aniso-data.png")
Out[11]:
In [12]:
Image("_g_aniso-conf.png")
Out[12]:
In [13]:
Image("_g_aniso-tcdf.png")
Out[13]:
In [14]:
Image("_g_aniso-vxcdf.png")
Out[14]:
In [15]:
Image("_g_aniso-vycdf.png")
Out[15]:
In [16]:
Image("_g_aniso-vzcdf.png")
Out[16]:
aniso_magic2.py¶
In [17]:
!aniso_magic2.py -f data_files/aniso_magic/dike_anisotropy.txt -gtc 110 2 -par -v -crd g \
-F data_files/aniso_magic/rmag_results.txt -fmt png -sav -n 300
In [18]:
Image(filename='Scripps Beach_g_TY__aniso-tcdf_.png')
Out[18]:
In [19]:
Image(filename='Scripps Beach_g_TY__aniso-data_.png')
Out[19]:
In [20]:
Image(filename='Scripps Beach_g_TY__aniso-conf_.png')
Out[20]:
apwp.py¶
In [21]:
!apwp.py -f data_files/apwp/apwp_example.dat
atrm_magic.py¶
In [22]:
if os.path.exists('data_files/atrm_magic/specimens.txt'):
os.remove('data_files/atrm_magic/specimens.txt')
!atrm_magic.py -WD data_files/atrm_magic -f atrm_measurements3.txt
!cat data_files/atrm_magic/specimens.txt | head
In [23]:
# with MagIC 2
!sio_magic2.py -f data_files/atrm_magic/atrm_magic_example.dat -loc Africa -LP T:ANI\
-F data_files/atrm_magic/atrm_measurements.txt -ncn 1 -dc 40 -1 -1
!atrm_magic.py -DM 2 -f data_files/atrm_magic/atrm_measurements.txt\
-Fa data_files/atrm_magic/trm_anisotropy.txt -Fr data_files/atrm_magic/atrm_results.txt
azdip_magic.py¶
In [24]:
# MagIC 3
!azdip_magic.py -f data_files/azdip_magic/azdip_magic_example.dat -ncn 1\
-mcd FS-FD:SO-POM -loc "Northern Iceland" -DM 3 -WD data_files/azdip_magic
!cat data_files/azdip_magic/samples.txt | head
In [25]:
# MagIC 2.5
!azdip_magic.py -f data_files/azdip_magic/azdip_magic_example.dat -ncn 1\
-mcd FS-FD:SO-POM -loc "Northern Iceland" -Fsa data_files/azdip_magic/er_samples.txt -DM 2
! cat data_files/azdip_magic/er_samples.txt | head
bgc_magic.py¶
In [26]:
!bgc_magic.py -f data_files/convert_2_magic/BGC_magic/15HHA1-2A
b_vdm.py¶
In [27]:
!b_vdm.py -f data_files/b_vdm/b_vdm_example.dat
bootams.py¶
In [28]:
!bootams.py -par -f data_files/bootams/bootams_example.dat -n 300
In [29]:
!bootams.py -f data_files/bootams/bootams_example.dat -n 300
cart_dir.py¶
In [30]:
!cart_dir.py -f data_files/cart_dir/cart_dir_example.dat
chartmaker.py¶
You can't do chartmaker from within the notebook. And chi_magic.py is still a bit buggy (problem with legend and 4th plot still shows up.)
chi_magic.py¶
In [31]:
!chi_magic.py -f data_files/chi_magic/measurements.txt -fmt png -sav
In [32]:
Image('IRM-OldBlue-1892_temperature.png')
Out[32]:
In [33]:
!chi_magic2.py -f data_files/chi_magic/chi_magic_example.dat -fmt png -sav
In [34]:
Image(filename='IRM-OldBlue-1892_1.png')
Out[34]:
In [35]:
Image(filename='IRM-OldBlue-1892_3.png')
Out[35]:
In [36]:
Image(filename='IRM-OldBlue-1892_2.png')
Out[36]:
cit_magic.py¶
In [37]:
!cit_magic.py -f data_files/convert_2_magic/cit_magic/PI47/PI47-.sam -loc "Slate Islands" \
-spc 1 -ncn 2 -mcd "FS-FD:SO-MAG" -A
combine_magic.py¶
MagIC tables have many columns only some of which are used in a particular instance. So combining files of the same type must be done carefully to ensure that the right data come under the right headings. The program combine_magic.py can be used to combine any number of MagIC files from a given type.
In [38]:
!combine_magic.py -WD data_files/combine_magic -F measurements.txt -f af_measurements.txt therm_measurements.txt
common_mean.py¶
In [39]:
!common_mean.py -f data_files/common_mean/common_mean_ex_file1.dat\
-f2 data_files/common_mean/common_mean_ex_file2.dat -sav -fmt png
In [40]:
Image(filename='CD_X.png')
Out[40]:
In [41]:
Image(filename='CD_Y.png')
Out[41]:
In [42]:
Image(filename='CD_Z.png')
Out[42]:
cont_rot.py¶
In [258]:
!cont_rot.py -con af:sam -prj ortho\
-eye -20 0 -sym k- 1 -age 180 -res l -fmt png -sav
In [44]:
if basemap_present:
image = Image(filename="Cont_rot.png")
else:
image = None
image
core_depthplot.py¶
In [45]:
# OSX users with pip install should use:
#!core_depthplot_anaconda -fsa data_files/core_depthplot/er_samples.txt -LP AF 15 \
# -f data_files/core_depthplot/magic_measurements.txt -log \
# -d 50 150 -ts gts12 23 34 -D -fmt png -sav -DM 2
# test with MagIC 2.5
!core_depthplot.py -fsa data_files/core_depthplot/er_samples.txt -LP AF 15 \
-f data_files/core_depthplot/magic_measurements.txt -log \
-d 50 150 -ts gts12 23 34 -D -fmt png -sav -DM 2
In [46]:
Image(filename='DSDP Site 522_m__LT-AF-Z_core-depthplot.png')
Out[46]:
In [47]:
# OSX users with pip install should use:
#!core_depthplot_anaconda -DM 3 -fsa ./data_files/core_depthplot/samples.txt -LP AF 15 \
# -f ./data_files/core_depthplot/measurements.txt -log \
# -d 50 150 -ts gts12 23 34 -D -fmt png -sav -DM 3 -ID ./data_files/core_depthplot
try:
os.remove('DSDP Site 522_m__LT-AF-Z_core-depthplot.png')
except FileNotFoundError:
pass
!core_depthplot.py -DM 3 -fsa ./data_files/core_depthplot/samples.txt -LP AF 15 \
-f ./data_files/core_depthplot/measurements.txt -log \
-d 50 150 -ts gts12 23 34 -D -fmt png -sav -DM 3 -ID ./data_files/core_depthplot
In [48]:
Image('DSDP Site 522_m__LT-AF-Z_core-depthplot.png')
Out[48]:
In [49]:
# OSX users with pip install should use:
#!core_depthplot_anaconda -DM 3 -fa ./data_files/core_depthplot/ages.txt -LP AF 15 \
# -f ./data_files/core_depthplot/measurements.txt -log \
# -ts gts12 23 34 -D -fmt png -sav -DM 3 -ID ./data_files/core_depthplot
try:
os.remove('DSDP Site 522_m__LT-AF-Z_core-depthplot.png')
except FileNotFoundError:
pass
!core_depthplot.py -DM 3 -fa ./data_files/core_depthplot/ages.txt -LP AF 15 \
-f ./data_files/core_depthplot/measurements.txt -log \
-ts gts12 23 34 -D -fmt png -sav -DM 3 -ID ./data_files/core_depthplot # not a meaningful option with age -d 50 150
In [50]:
Image('DSDP Site 522_m__LT-AF-Z_core-depthplot.png')
Out[50]:
curie.py¶
In [51]:
!curie.py -f data_files/curie/curie_example.dat -w 10 -fmt png -sav
In [52]:
Image(filename='M_T.png')
Out[52]:
dayplot_magic.py¶
In [53]:
!dayplot_magic.py -WD data_files/dayplot_magic -f specimens.txt -sav -fmt png
In [54]:
Image("_day.png")
Out[54]:
dayplot_magic2.py¶
In [55]:
!dayplot_magic2.py -WD data_files/dayplot_magic/ -f dayplot_magic_example.dat \
-fmt png -sav
In [56]:
Image(filename='unknown_day.png')
Out[56]:
demag_gui.py¶
Use demag_gui.py from the command line or from within pmag_gui.py (Pmag GUI).
di_eq.py¶
In [57]:
!di_eq.py -f data_files/di_eq/di_eq_example.dat
di_geo.py¶
In [58]:
!di_geo.py -f data_files/di_geo/di_geo_example.dat -F data_files/di_geo/di_geo.out
!cat data_files/di_geo/di_geo.out | head
di_rot.py¶
In [59]:
!eqarea.py -f data_files/di_rot/di_rot_example.txt -fmt png -sav
Image(filename='di_rot_example_eq.png')
Out[59]:
In [60]:
!di_rot.py -f data_files/di_rot/di_rot_example.txt -F data_files/di_rot/dirot.out -D 359.3 -I 42.1
!eqarea.py -f data_files/di_rot/dirot.out -fmt png -sav
In [61]:
Image(filename='dirot_eq.png')
Out[61]:
di_tilt.py¶
In [62]:
!di_tilt.py < data_files/di_tilt/di_tilt_example.dat
di_vgp.py¶
In [63]:
!di_vgp.py -f data_files/di_vgp/di_vgp_example.dat
dipole_pinc.py¶
In [64]:
!dipole_pinc.py -f data_files/dipole_pinc/dipole_pinc_example.dat
dipole_plat.py¶
In [65]:
!dipole_plat.py -f data_files/dipole_plat/dipole_plat_example.dat
dir_cart.py¶
In [66]:
!dir_cart.py -f data_files/dir_cart/dir_cart_example.dat
dmag_magic.py¶
In [67]:
!dmag_magic.py -WD data_files/3_0/McMurdo -fsp specimens.txt -obj spc -sav -fmt "png" -LT T
In [68]:
Image(filename="mc01a_LT-T-Z.png")
Out[68]:
In [69]:
Image("mc141c1_LT-T-Z.png")
Out[69]:
In [70]:
!dmag_magic.py -WD data_files/3_0/McMurdo -fsp specimens.txt \
-fsa samples.txt -obj sit -sav -fmt "png" -LT T
In [71]:
Image(filename="mc01_LT-T-Z.png")
Out[71]:
dmag_magic2.py¶
In [72]:
!dmag_magic2.py -f data_files/dmag_magic/dmag_magic_example.dat -LT AF -fmt png -sav
In [73]:
Image(filename='McMurdo_LT-AF-Z.png')
Out[73]:
download_magic.py¶
In [74]:
!download_magic.py -WD data_files/download_magic -f data_files/download_magic/magic_contribution_16503.txt
eigs_s.py¶
In [75]:
!eigs_s.py -f data_files/eigs_s/eigs_s_example.dat
eq_di.py¶
In [76]:
!eq_di.py -f data_files/eq_di/eq_di_example.dat > data_files/eq_di/eq_di.out
!eqarea.py -f data_files/eq_di/eq_di.out -fmt png -sav
In [77]:
Image(filename='eq_di_eq.png')
Out[77]:
eqarea.py¶
In [78]:
!eqarea.py -f data_files/eqarea/fishrot.out -fmt png -sav
In [79]:
Image(filename='fishrot_eq.png')
Out[79]:
eqarea_ell.py¶
In [80]:
!eqarea_ell.py -f data_files/eqarea_ell/tk03.out -ell B -fmt png -sav
In [81]:
Image(filename='data_files-eqarea_ell-tk03.out_eq.png')
Out[81]:
eqarea_magic.py¶
In [82]:
!eqarea_magic.py -WD data_files/3_0/McMurdo -f sites.txt -sav -fmt "png"
In [83]:
Image(filename="all_McMurdo_g_eqarea.png")
Out[83]:
In [84]:
!download_magic.py -WD data_files/nrm_specimens_magic \
-f data_files/nrm_specimens_magic/magic_contribution_15143.txt -DM 3
In [85]:
# plot by specimen
!eqarea_magic.py -f data_files/nrm_specimens_magic/nrm_specimens.txt -crd g -fmt png -sav -obj spc
Image('Snake_River_sr42_sr42b_sr42b1_g_eqarea.png')
Out[85]:
In [86]:
# plotting all with no sites file
# get rid of any png files lying around
for fname in glob.glob("*.png"):
os.remove(fname)
# temporarily hide sites file
try:
os.rename('data_files/nrm_specimens_magic/sites.txt', 'data_files/nrm_specimens_magic/temp.txt')
except FileNotFoundError:
pass
# run eqarea_magic
!eqarea_magic.py -f data_files/nrm_specimens_magic/nrm_specimens.txt -crd g -fmt png -sav -obj all
Image('all_g_eqarea.png')
Out[86]:
In [87]:
# plotting by sample with no sites file
# get rid of any png files lying around
for fname in glob.glob("*.png"):
os.remove(fname)
!eqarea_magic.py -f data_files/nrm_specimens_magic/nrm_specimens.txt -crd g -fmt png -sav -obj sam
Image('sr42_sr42b_g_eqarea.png')
Out[87]:
In [88]:
# can't get site data with no site or sample file, will fail gracefully
!mv data_files/nrm_specimens_magic/samples.txt data_files/nrm_specimens_magic/temp_samples.txt
!eqarea_magic.py -f data_files/nrm_specimens_magic/nrm_specimens.txt -crd g -fmt png -sav -obj sit
!mv data_files/nrm_specimens_magic/temp_samples.txt data_files/nrm_specimens_magic/samples.txt
In [89]:
# plotting by sample
# get rid of any png files lying around
for fname in glob.glob("*.png"):
os.remove(fname)
try:
os.rename('data_files/nrm_specimens_magic/temp.txt', 'data_files/nrm_specimens_magic/sites.txt')
except FileNotFoundError:
pass
!eqarea_magic.py -f data_files/nrm_specimens_magic/nrm_specimens.txt -crd g -fmt png -sav -obj sam
Image('Snake_River_sr42_sr42b_g_eqarea.png')
Out[89]:
In [90]:
# plotting all
for fname in glob.glob("*.png"):
os.remove(fname)
!eqarea_magic.py -WD data_files/nrm_specimens_magic/ -f nrm_specimens.txt -crd g -fmt png -sav -obj all
Image('all_Snake_River_g_eqarea.png')
Out[90]:
In [91]:
# using unknown option for -obj, will default to plotting all instead
for fname in glob.glob("*.png"):
os.remove(fname)
!eqarea_magic.py -f data_files/nrm_specimens_magic/samples.txt -crd g -fmt png -sav -obj loc # will use 'all'
Image('all_Snake_River_g_eqarea.png')
Out[91]:
eqarea_magic2.py¶
In [92]:
!eqarea_magic2.py -obj loc -crd g -f data_files/eqarea_magic/pmag_results.txt\
-ell Be -fmt png -sav
In [93]:
Image(filename='Snake_River_gu_eqarea.png')
Out[93]:
find_ei.py¶
In [94]:
!find_ei.py -f data_files/find_EI/find_EI_example.dat -fmt png -sav -n 300
In [95]:
Image(filename='findEI_ei.png')
Out[95]:
In [96]:
Image(filename='findEI_cdf.png')
Out[96]:
In [97]:
Image(filename='findEI_eq.png')
Out[97]:
In [98]:
Image(filename='findEI_v2.png')
Out[98]:
fisher.py¶
In [99]:
!fisher.py -k 30 -n 10
fishqq.py¶
In [100]:
!fishqq.py -f data_files/fishqq/fishqq_example.txt -fmt png -sav
In [101]:
Image(filename='data_files-fishqq-fishqq_example.txt_unf1.png')
Out[101]:
In [102]:
Image(filename='data_files-fishqq-fishqq_example.txt_exp1.png')
Out[102]:
fishrot.py¶
In [103]:
!fishrot.py -n 5 -D 33 -I 41 -k 50
foldtest.py¶
In [104]:
!foldtest.py -f data_files/foldtest/foldtest_example.dat -fmt png -sav -n 300
In [105]:
Image(filename='foldtest_ta.png')
Out[105]:
In [106]:
Image(filename='foldtest_st.png')
Out[106]:
In [107]:
Image(filename='foldtest_ge.png')
Out[107]:
foldtest_magic.py¶
In [108]:
!foldtest_magic.py -f data_files/foldtest_magic/sites.txt -fmt png -sav -DM 3 -n 300 -exc
In [109]:
Image(filename='foldtest_ge.png')
Out[109]:
In [110]:
!download_magic.py -WD data_files/foldtest_magic -f data_files/foldtest_magic/magic_contribution_11087.txt
In [111]:
!foldtest_magic.py -f data_files/foldtest_magic/pmag_sites.txt \
-fsi data_files/foldtest_magic/er_sites.txt -fmt png -sav -DM 2 -n 300
In [112]:
Image(filename='foldtest_ge.png')
Out[112]:
In [113]:
Image(filename='foldtest_st.png')
Out[113]:
In [114]:
Image(filename='foldtest_ta.png')
Out[114]:
forc_diagram.py¶
In [115]:
!forc_diagram.py -f data_files/forc_diagram/conventional_example.forc -sf 3 -sav -fmt png
Image('forc.png')
Out[115]:
gaussian.py¶
In [116]:
!gaussian.py -s 3 -n 1000 -m 10. -F data_files/gaussian/gaussian.out
!histplot.py -f data_files/gaussian/gaussian.out -fmt png -sav
In [117]:
Image(filename='hist.png')
Out[117]:
generic_magic.py¶
In [118]:
!generic_magic.py -f data_files/convert_2_magic/generic_magic/generic_magic_example.txt -exp PI
gobing.py¶
In [119]:
!gobing.py -f data_files/gobing/gobing_example.txt
gofish.py¶
In [120]:
!gofish.py -f data_files/gofish/fishrot.out
gokent.py¶
In [121]:
!gokent.py -f data_files/gokent/gokent_example.txt
goprinc.py¶
In [122]:
!goprinc.py -f data_files/goprinc/tk03.out
grab_magic_key.py¶
In [123]:
!grab_magic_key.py -f data_files/download_magic/sites.txt -key lat
huji_magic.py¶
In [124]:
!huji_magic.py -f data_files/convert_2_magic/HUJI_magic/Massada_AF_HUJI_new_format.txt -LP T
huji_sample_magic.py¶
In [125]:
!huji_sample_magic.py -f data_files/convert_2_magic/HUJI_magic/magdelkrum_datafile.txt
hysteresis_magic.py¶
In [126]:
# for MagIC data model 3:
!hysteresis_magic.py -WD data_files/hysteresis_magic/ -f measurements.txt \
-spc IS06a-1 -fmt png -sav
In [127]:
Image(filename='IS06a-1_hyst.png')
Out[127]:
In [128]:
Image('IS06a-1_deltaM.png')
Out[128]:
In [129]:
# For MagIC data model 2:
!hysteresis_magic2.py -WD data_files/hysteresis_magic/ -f hysteresis_magic_example.dat \
-spc IS06a-1 -fmt png -sav
In [130]:
Image(filename='_IS06a-1_hyst.png')
Out[130]:
In [131]:
!hysteresis_magic.py -WD data_files/hysteresis_magic/ -f measurements.txt \
-spc IS06a-1 -fmt png -sav
In [132]:
Image(filename='IS06a-1_hyst.png')
Out[132]:
iodp_dscr_magic.py¶
In [133]:
!iodp_dscr_magic.py -f data_files/convert_2_magic/IODP_srm_magic/IODP_LIMS_SRMdiscrete_344_1414A.csv
iodp_jr6_magic.py¶
In [134]:
!iodp_jr6_magic.py -f data_files/convert_2_magic/IODP_jr6_magic/test.jr6
iodp_srm_magic.py¶
In [135]:
!iodp_srm_magic.py -f data_files/convert_2_magic/iodp_srm_magic/SRM_318_U1359_B_A.csv
igrf.py¶
In [136]:
!igrf.py -ages -3000 1950 50 -loc 33 -117 -mod pfm9k -plt -fmt png -sav
In [137]:
Image(filename='igrf.png')
Out[137]:
install_etopo.py¶
In [138]:
# install high resolution maps, only used for Basemap
!install_etopo.py
incfish.py¶
In [139]:
!incfish.py -f data_files/incfish/incfish_example_inc.dat
irmaq_magic.py¶
In [140]:
!sio_magic.py -f data_files/irmaq_magic/U1359A_IRM_coil2.txt -LP I -V 2 \
-WD data_files/irmaq_magic/ -F U1359A_IRM_coil2.magic -loc U1359A -spc 0 -ncn 5 \
-Fsp coil2_specimens.txt -Fsa coil2_samples.txt -Fsi coil2_sites.txt -Flo coil2_locations.txt
!sio_magic.py -f data_files/irmaq_magic/U1359A_IRM_coil3.txt -LP I -V 3 \
-WD data_files/irmaq_magic/ -F U1359A_IRM_coil3.magic -loc U1359A -spc 0 -ncn 5 \
-Fsp coil3_specimens.txt -Fsa coil3_samples.txt -Fsi coil3_sites.txt -Flo coil3_locations.txt
!combine_magic.py -F data_files/irmaq_magic/measurements.txt \
-f data_files/irmaq_magic/U1359A_IRM_coil2.magic \
data_files/irmaq_magic/U1359A_IRM_coil3.magic -dm 3
!combine_magic.py -F measurements.txt -WD data_files/irmaq_magic \
-f U1359A_IRM_coil2.magic U1359A_IRM_coil3.magic -dm 3
!combine_magic.py -F specimens.txt -WD data_files/irmaq_magic \
-f coil2_specimens.txt coil3_specimens.txt
!combine_magic.py -F samples.txt -WD data_files/irmaq_magic \
-f coil2_samples.txt coil3_samples.txt
!combine_magic.py -F sites.txt -WD data_files/irmaq_magic \
-f coil2_sites.txt coil3_sites.txt
!combine_magic.py -F locations.txt -WD data_files/irmaq_magic \
-f coil2_locations.txt coil3_locations.txt
In [141]:
!irmaq_magic.py -f data_files/irmaq_magic/measurements.txt -fmt png -sav -DM 3
In [142]:
Image("U1359A_LP-IRM.png")
Out[142]:
irmaq_magic.py (data model 2)¶
In [143]:
!sio_magic2.py -f data_files/irmaq_magic/U1359A_IRM_coil2.txt -LP I -V 2 \
-F data_files/irmaq_magic/U1359A_IRM_coil2.magic -loc U1359A -spc 0 -ncn 5
!sio_magic2.py -f data_files/irmaq_magic/U1359A_IRM_coil3.txt -LP I -V 3 \
-F data_files/irmaq_magic/U1359A_IRM_coil3.magic -loc U1359A -spc 0 -ncn 5
!combine_magic.py -F data_files/irmaq_magic/magic_measurements.txt \
-f data_files/irmaq_magic/U1359A_IRM_coil2.magic \
data_files/irmaq_magic/U1359A_IRM_coil3.magic -dm 2
In [144]:
!irmaq_magic.py -f data_files/irmaq_magic/magic_measurements.txt -fmt png -sav -DM 2
In [145]:
Image(filename='U1359A_LP-IRM.png')
Out[145]:
jr6_jr6_magic.py¶
In [146]:
!jr6_jr6_magic.py -f data_files/convert_2_magic/JR6_magic/AF.jr6
jr6_txt_magic.py¶
In [147]:
!jr6_txt_magic.py -f data_files/convert_2_magic/JR6_magic/AF.txt
k15_magic.py¶
In [148]:
!k15_magic.py -WD data_files/k15_magic -spc 0 -f data_files/k15_s/k15_example.dat -loc "Troodos Ophiolite"
In [149]:
!k15_s.py -f data_files/k15_s/k15_example.dat
kly4s_magic.py¶
In [150]:
!kly4s_magic.py -f data_files/convert_2_magic/kly4s_magic/KLY4S_magic_example.dat
ldeo_magic.py¶
In [151]:
!ldeo_magic.py -f data_files/convert_2_magic/LDEO_magic/ldeo_magic_example.dat
livdb_magic.py¶
In [152]:
# is a GUI and doesn't work in a notebook
# see _PmagPy-nb.ipynb for how to use convert.livdb
lnp_magic.py¶
In [153]:
!lnp_magic.py -f data_files/lnp_magic/specimens.txt -crd g -fmt png -sav -fsa data_files/lnp_magic/samples.txt
In [154]:
Image(filename='sv01_g_eqarea.png')
Out[154]:
In [155]:
os.remove('sv01_g_eqarea.png')
In [156]:
!download_magic.py -WD data_files/lnp_magic -ID data_files/lnp_magic -f zmab0001193tmp02.txt
In [157]:
!lnp_magic.py -f data_files/lnp_magic/pmag_specimens.txt -crd g -fmt png -sav -DM 2
In [158]:
Image(filename='sv01_g_eqarea.png')
Out[158]:
lowes.py doesn't work from within a notebook. yet.
lowrie.py¶
In [159]:
!lowrie.py -f data_files/lowrie/lowrie_example.dat -fmt png -sav
In [160]:
Image(filename='lowrie__318-U1359A-002H-1-W-109_.png')
Out[160]:
lowrie_magic.py¶
In [161]:
!lowrie_magic.py -f data_files/lowrie_magic/measurements.txt -fmt png -sav
In [162]:
Image("lowrie__318-U1361A-008H-6-W-83a_.png")
Out[162]:
In [163]:
!lowrie_magic.py -f data_files/lowrie_magic/lowrie_magic_example.dat -fmt png -sav -DM 2
In [164]:
Image(filename='lowrie__318-U1359A-002H-1-W-109_.png')
Out[164]:
magic_select.py¶
In [165]:
!magic_select.py -f data_files/magic_select/pmag_specimens.txt \
-key magic_method_codes LP-DIR-AF has -F data_files/magic_select/AF_specimens.txt
mini_magic.py¶
In [166]:
!mini_magic.py -WD data_files/convert_2_magic/mini_magic -f Peru_rev1.txt
mst_magic.py¶
In [167]:
!mst_magic.py -f data_files/convert_2_magic/MsT_magic/curie_example.dat -spn specimen_name
mk_redo.py¶
In [168]:
!mk_redo.py -WD data_files/mk_redo
In [169]:
!cat data_files/mk_redo/thellier_redo | head
In [170]:
!cat data_files/mk_redo/zeq_redo | head
orientation_magic.py¶
In [171]:
try:
os.remove('data_files/orientation_magic/samples.txt')
except FileNotFoundError:
pass
!orientation_magic.py -WD data_files/orientation_magic -f orient_example.txt -gmt 13
!cat data_files/orientation_magic/samples.txt | head
pca.py¶
In [172]:
!pca.py -dir L 1 10 -f data_files/pca/pca_example.txt
pmd_magic.py¶
In [173]:
!pmd_magic.py -f data_files/convert_2_magic/PMD_magic/PMD/ss0207a.pmd
plotxy.py¶
In [174]:
!plotxy.py -f data_files/plotXY/plotXY_example.txt -fmt png -sav
In [175]:
Image(filename='plotXY.png')
Out[175]:
plot_cdf.py¶
In [176]:
!plot_cdf.py -f data_files/plot_cdf/gaussian.out -fmt png -sav
In [177]:
Image(filename='CDF_.png')
Out[177]:
plot_geomagia.py doesn't work on the command line - see _PmagPy_nb example.
plot_magmap.py¶
In [178]:
!plot_magmap.py -el B -fmt png -sav
In [179]:
image = None
if cartopy_present:
image = Image('geomagnetic_field_2016.0.png')
image
Out[179]:
plot_map_pts.py¶
In [180]:
!plot_map_pts.py -f data_files/plot_map_pts/uniform.out -B -R \
-prj ortho -eye 30 0 -etp -sym wo 10 -fmt png -sav
In [181]:
image = None
if cartopy_present:
image = Image(filename='map_pts.png')
image
Out[181]:
plotdi_a.py¶
In [182]:
!plotdi_a.py -f data_files/plotdi_a/plotdi_a_example.dat -fmt png -sav
In [183]:
Image(filename='eq.png')
Out[183]:
pmag_results_extract.py¶
In [184]:
!pmag_results_extract.py -WD data_files/pmag_results_extract -f pmag_results.txt
polemap_magic.py¶
In [185]:
!polemap_magic.py -WD data_files/polemap_magic -sav -fmt png
In [186]:
image = None
if cartopy_present:
image = Image(filename="Skaistgirys Carbonates_Cismon Section_Monte Raparo_POLE_map.png")
image
Out[186]:
pt_rot.py¶
In [187]:
!awk '{print $1,$2}' data_files/pt_rot/pt_rot.input > data_files/pt_rot/lon_lat
!plot_map_pts.py -prj moll -f data_files/pt_rot/lon_lat -sym g^ 10 -R -B -eye 0 0 -fmt png -sav
In [188]:
image
if cartopy_present:
image = Image(filename='map_pts.png')
image
Out[188]:
In [189]:
!cat data_files/pt_rot/pt_rot.input
!pt_rot.py -f data_files/pt_rot/pt_rot.input > data_files/pt_rot/pt_rot.out
In [190]:
!plot_map_pts.py -prj moll -f data_files/pt_rot/pt_rot.out -sym ro 10 -R -B -eye 0 0 -fmt png -sav
In [191]:
if cartopy_present:
image = Image(filename='map_pts.png')
image
Out[191]:
Something still weird about pt_rot.py (the -ff option).
In [192]:
!pt_rot.py -ff data_files/pt_rot/nam_180-200.txt data_files/pt_rot/nam_panA.frp > data_files/pt_rot/pt_rot_panA.out
In [193]:
!plot_map_pts.py -f data_files/pt_rot/pt_rot_panA.out -prj ortho -eye 60 90 -sym ro 10 -B -R -fmt png -sav
In [194]:
image = None
if cartopy_present:
image = Image(filename='Map_pts.png')
image
Out[194]:
qqplot.py¶
In [195]:
!qqplot.py -f data_files/qqplot/gauss.out -fmt png -sav
In [196]:
Image(filename='qq.png')
Out[196]:
quick_hyst.py¶
In [197]:
!quick_hyst.py -WD data_files/3_0/McMurdo -spc mc04c-1 -fmt png
Image("McMurdo_mc04c_mc04c_mc04c-1_hyst.png")
Out[197]:
quick_hyst2.py¶
In [198]:
!quick_hyst2.py -f data_files/hysteresis_magic/hysteresis_magic_example.dat -fmt png -sav
In [199]:
Image(filename='IS06_IS06a_IS06a-1_hyst.png')
Out[199]:
revtest.py¶
In [200]:
!revtest.py -f data_files/revtest/revtest_example.txt -fmt png -sav
In [201]:
Image(filename='REV_X.png')
Out[201]:
In [202]:
Image(filename='REV_Y.png')
Out[202]:
In [203]:
Image(filename='REV_Z.png')
Out[203]:
revtest_magic.py¶
In [204]:
!revtest_magic.py -f data_files/revtest_magic/sites.txt -fmt png -sav -DM 3 -exc
In [205]:
Image("Rev_Y.png")
Out[205]:
In [206]:
!revtest_magic.py -f data_files/revtest_magic/revtest_magic_example.txt -fmt png -sav -DM 2
In [207]:
Image(filename='REV_X.png')
Out[207]:
s_eigs.py¶
In [208]:
!s_eigs.py -f data_files/s_eigs/s_eigs_example.dat
s_geo.py¶
In [209]:
!s_geo.py -f data_files/s_geo/s_geo_example.dat
s_hext.py¶
In [210]:
!s_geo.py -f data_files/s_geo/s_geo_example.dat | s_hext.py
sio_magic.py¶
See irmaq_magic.py
s_tilt.py¶
In [211]:
!s_tilt.py -f data_files/s_tilt/s_tilt_example.dat
s_magic.py¶
In [212]:
!s_magic.py -WD data_files/convert_2_magic/s_magic -f s_magic_example.dat
scalc.py¶
In [213]:
!scalc.py -f data_files/scalc/scalc_example.txt
In [214]:
!scalc.py < data_files/scalc/scalc_example.txt
In [215]:
!scalc.py -f data_files/scalc/scalc_example.txt -v
In [216]:
!scalc.py -f data_files/scalc/scalc_example.txt -v -b
scalc_magic.py¶
In [217]:
!scalc_magic.py -f data_files/scalc_magic/sites.txt -c 30
In [218]:
!scalc_magic.py -f data_files/scalc_magic/pmag_results.txt -c 30 -dm 2
site_edit.py¶
This program requires user interaction and can only be used on the command line.
specimens_results_magic.py¶
This program has been superceded by Pmag GUI and is not maintained.
stats.py¶
In [219]:
!stats.py -f data_files/gaussian/gauss.out
strip_magic.py¶
In [220]:
!strip_magic.py -f data_files/strip_magic/pmag_results.txt -x age -y lat -fmt png -sav -DM 2
In [221]:
Image(filename='strat.png')
Out[221]:
In [222]:
!rm strat.png
!strip_magic.py -f data_files/strip_magic/sites_with_vgps.txt -x age -y lat -fmt png -sav -DM 3
In [223]:
Image(filename='strat.png')
Out[223]:
sundec.py¶
In [224]:
!sundec.py -f data_files/sundec/sundec_example.dat
thellier_magic.py¶
This program is no longer maintained - try Thellier GUI instead.
thellier_magic_redo.py¶
The function of this program has been incorporated into Thellier GUI so you should use that instead.
tk03.py¶
In [225]:
!tk03.py -lat 30 > data_files/tk03/tk03.out
!eqarea.py -f data_files/tk03/tk03.out -fmt png -sav
In [226]:
Image(filename='tk03_eq.png')
Out[226]:
trmaq_magic.py¶
In [227]:
!trmaq_magic.py -ft data_files/3_0/McMurdo/specimens.txt \
-f data_files/3_0/McMurdo/measurements.txt -sav -fmt png
In [228]:
Image("mc117b1_TRM.png")
Out[228]:
In [229]:
!rm mc117b1_TRM.png
!trmaq_magic.py -ft data_files/2_5/McMurdo/pmag_specimens.txt \
-f data_files/2_5/McMurdo/magic_measurements.txt -sav -fmt png -DM 2
In [230]:
Image("mc117b1_TRM.png")
Out[230]:
uniform.py¶
In [231]:
!uniform.py -n 50
In [232]:
!uniform.py -n 50 > data_files/uniform/uniform.out
!eqarea.py -f data_files/uniform/uniform.out -fmt png -sav
In [233]:
Image(filename='uniform_eq.png')
Out[233]:
update_measurements.txt¶
This program has been superceded by Pmag GUI, so you should use that.
utrecht_magic.py¶
In [234]:
!utrecht_magic.py -f data_files/convert_2_magic/UTRECHT_magic/Utrecht_Example.af
vdm_b.py¶
In [235]:
!vdm_b.py -f data_files/vdm_b/vdm_b_example.dat
In [236]:
!cat data_files/b_vdm/b_vdm_example.dat
vector_mean.py¶
In [237]:
!vector_mean.py -f data_files/vector_mean/vector_mean_example.dat
vgp_di.py¶
In [238]:
!vgp_di.py -f data_files/vgp_di/vgp_di_example.dat
vgpmap_magic.py¶
In [239]:
!vgpmap_magic.py -WD data_files/3_0/McMurdo -f sites.txt -crd g -prj ortho -eye 60 0 -sym ko 10 -fmt png -S -sav
In [240]:
image = None
if cartopy_present:
image = Image("McMurdo_VGP_map.png")
image
Out[240]:
vgpmap_magic2.py¶
In [241]:
# MagIC 2 version of vgpmap_magic.py
!vgpmap_magic2.py -f data_files/vgpmap_magic/pmag_results.txt \
-crd g -prj ortho -eye 60 0 -etp -sym wo 10 -fmt png -sav
In [242]:
if cartopy_present:
image = Image(filename='Snake_River_VGP_map.png')
else:
image = None
image
Out[242]:
watsons_f.py¶
In [243]:
!watsons_f.py -f data_files/watsons_f/watsons_f_example_file1.dat \
-f2 data_files/watsons_f/watsons_f_example_file2.dat
watsons_v.py¶
In [244]:
!watsons_v.py -f data_files/watsons_f/watsons_f_example_file1.dat \
-f2 data_files/watsons_f/watsons_f_example_file2.dat -fmt png -sav
In [245]:
Image(filename="watsons_v_watsons_f_example_file1_watsons_f_example_file2.png")
Out[245]:
zeq.py¶
This program requires interaction and can only be run from the command line.
In [246]:
!zeq_magic.py -WD data_files/3_0/McMurdo -spc mc01a -fmt png
Image('mc01a_eqarea.png')
Out[246]:
cleanup the directory¶
In [247]:
import os
import glob
import shutil
glob_list = ['data_files/irmaq_magic/*.magic', '*.magic', '*.png', '*.jpg',
'data_files/convert_2_magic/mini_magic/s*.txt', 'data_files/convert_2_magic/s_magic/*.txt',
'data_files/irmaq_magic/coil*.txt', 'rmag_*.txt', 'data_files/orientation_magic/s*.txt',
'data_files/mk_redo/*redo*', 'data_files/nrm_specimens_magic/s*.txt', 'data_files/irmaq_magic/s*.txt',
'data_files/download_magic/pmag_s*.txt', 'data_files/convert_2_magic/tdt_magic/*.txt']
for pattern in glob_list:
for fname in glob.glob(pattern):
os.remove(fname)
files_to_remove = ["data_files/aarm_magic/aarm_measurements.txt", "data_files/irmaq_magic/magic_measurements.txt",
"data_files/download_magic/er_ages.txt", "data_files/download_magic/er_citations.txt",
"data_files/azdip_magic/er_samples.txt", "data_files/azdip_magic/samples.txt",
"data_files/convert_2_magic/mini_magic/locations.txt",
"data_files/convert_2_magic/mini_magic/measurements.txt", "measurements.txt", 'specimens.txt',
'sites.txt', 'locations.txt', 'stored.json', 'data_files/nrm_specimens_magic/criteria.txt',
'data_files/download_magic/er_locations.txt', 'data_files/download_magic/pmag_results.txt',
'data_files/nrm_specimens_magic/measurements.txt', 'data_files/nrm_specimens_magic/locations.txt',
'data_files/nrm_specimens_magic/contribution.txt', 'data_files/nrm_specimens_magic/ages.txt',
'data_files/irmaq_magic/locations.txt', 'data_files/download_magic/specimens.txt',
'data_files/download_magic/samples.txt', 'data_files/download_magic/locations.txt',
'data_files/download_magic/contribution.txt', 'data_files/download_magic/criteria.txt',
'data_files/download_magic/ages.txt', 'data_files/download_magic/measurements.txt',
'data_files/convert_2_magic/tdt_magic/custom.out', 'custom.txt',
'data_files/convert_2_magic/huji_magic/specimens.txt',
'data_files/convert_2_magic/huji_magic/locations.txt', 'data_files/aarm_magic/measurements.txt']
for fname in files_to_remove:
try:
os.remove(fname)
except FileNotFoundError:
pass
for dtype in ['specimens.txt', 'samples.txt', 'sites.txt', 'locations.txt']:
try:
os.remove(dtype)
except FileNotFoundError:
pass
for fname in os.listdir():
if fname.endswith(dtype):
os.remove(fname)